W09: Building Ontologies with Basic Formal Ontology

ICBO2018 Workshop-W09

Organizer(s):

Barry Smith

Workshop type:

Tutorial/Demo

Workshop Abstract

Overview Description of Contents Part 1: General Introduction We will begin by describing how BFO is used in building ontologies, including a brief description and review of BFO’s role in ontologies such as: Information Artifact Ontology (IAO) Ontology for Biomedical Investigations (OBI) Protein Sites Ontology (branch of PRO) Population and Community Ontology (PCO) Environment Ontology (ENVO) Ontology of Medically Relevant Social Entities (OMRSE) Plant Ontology (PO) We will then review issues identified by users regarding the use BFO, paying particular attention to the use of defined classes in the treatment of process attributes, and the treatment of time and relations.

Part 2: BFO Draft International Standard ISO/IEC 21838-2 We will review the BFO Draft International Standard created by the International Standards Organization (ISO) to promote ontology-based interoperability of data and information systems. We will summarize how ISO and ISO standards work, and outline some of the opportunities that will be created by this new standard for current and future users of BFO. We will also outline how the standard deals with different versions of BFO in OWL, Common Logic (CL).

Part 3: Review of BFO Current Extension Proposals (Interactive Section) A number of proposals are under consideration for the addition of new terms to BFO or for the creation of new mid-level BFO-conformant extension ontologies analogous to the Information Artifact Ontology (IAO). This part of the tutorial will take the form of an interactive session in which three of these proposals will be subjected to critical review. i. Ontology of Social Interactions: The first set of proposals concerns the creation of an over-arching ontology for entities in the realm of human social interactions, drawing on the Population and Community Ontology (PCO), the Document Acts Ontology (D-acts), and the Ontology of Medically Relevant Social Entities (OMRSE). ii. Ontology of Capabilities: The second set of proposals concerns the topic of capabilities, and specifically the proposal to identify capabilities as a universal intermediate between functions and dispositions. Every function, on this proposal, would be a capability, and every capability a disposition. Examples of human capabilities are skills, including language skills or diagnosing skills. Examples of machine capabilities are the safety features of your car. iii. Ontology of Systems: The third set of proposals concerns the topic of biological systems such as your cardiovascular system or the tropical rainforest biome. We will explore the question of how to define ‘system’, drawing on definitions developed by ENVO and PCO of terms such as ‘ecological system’, ‘habitat’, and ‘biome’. We will conclude with an exploration of the potential of such definitions to form the basis of an ontology of the microbiome as an ecosystem determined by populations of microbiota.

Rational:

BFO is an ontology that is being used by some 300 different groups in biology and biomedicine to provide a top-level architecture and starting point for definitions. Increasingly, ontology is being incorporated as top-level ontology in suites of ontology modules and this has led to the endorsement of BFO by the International Standards Organization as ISO standard ISO/IEC 21838-2. This tutorial is divided into two parts. The first is designed to familiarize actual and potential users of BFO with the implications of these developments. The second is an interactive session that will provide an opportunity for critical review of a series of proposed additions and extensions of BFO.